LAMMPS (4 May 2022)
  using 1 OpenMP thread(s) per MPI task
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin

# settings

variable        x equal 10
variable        y equal 10
variable        z equal 20

variable        rho equal 0.6
variable        t equal 1.35
variable        rc equal 2.5
variable        tlo equal 1.0
variable        thi equal 1.70

#variable       rho equal 0.85
#variable        t equal 0.7
#variable       rc equal 3.0
#variable        tlo equal 0.3
#variable        thi equal 1.0

# setup problem

units           lj
atom_style      atomic

lattice         fcc ${rho}
lattice         fcc 0.6
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
region          box block 0 $x 0 $y 0 $z
region          box block 0 10 0 $y 0 $z
region          box block 0 10 0 10 0 $z
region          box block 0 10 0 10 0 20
create_box      1 box
Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
  2 by 1 by 4 MPI processor grid
create_atoms    1 box
Created 8000 atoms
  using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
  create_atoms CPU = 0.000 seconds
mass            1 1.0

velocity        all create $t 87287
velocity        all create 1.35 87287

pair_style      lj/cut ${rc}
pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0

neighbor        0.3 bin
neigh_modify    delay 0 every 1

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 10 11
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp $t $t 0.5
fix             1 all nvt temp 1.35 $t 0.5
fix             1 all nvt temp 1.35 1.35 0.5
thermo          100
run             1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 14 14 27
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.35          -4.1241917      0             -2.0994448     -3.1961612    
       100   1.1819832     -3.7640881      0             -1.991335       0.53985757   
       200   1.2578365     -3.7395333      0             -1.8530144      0.69591862   
       300   1.3282971     -3.7215427      0             -1.7293461      0.79036065   
       400   1.3714367     -3.7043826      0             -1.6474847      0.85873226   
       500   1.3590952     -3.6707735      0             -1.6323855      0.99602024   
       600   1.3575117     -3.7118244      0             -1.6758114      0.81454305   
       700   1.3284444     -3.7075488      0             -1.7151313      0.81136596   
       800   1.3419995     -3.7155648      0             -1.7028172      0.82925676   
       900   1.3562214     -3.6965609      0             -1.6624831      0.88908117   
      1000   1.3732017     -3.7100044      0             -1.6504594      0.83982701   
Loop time of 0.988841 on 8 procs for 1000 steps with 8000 atoms

Performance: 436874.916 tau/day, 1011.285 timesteps/s
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.54855    | 0.56275    | 0.57326    |   1.1 | 56.91
Neigh   | 0.25337    | 0.2589     | 0.26473    |   0.7 | 26.18
Comm    | 0.096617   | 0.10927    | 0.11899    |   2.2 | 11.05
Output  | 0.00032266 | 0.00051276 | 0.0018134  |   0.0 |  0.05
Modify  | 0.034998   | 0.042756   | 0.055888   |   4.0 |  4.32
Other   |            | 0.01466    |            |       |  1.48

Nlocal:           1000 ave        1020 max         982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost:         2299.5 ave        2331 max        2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs:          27122 ave       28382 max       26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1

Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0

velocity        all scale $t
velocity        all scale 1.35

unfix           1

# 2nd equilibration run

fix             1 all nve
fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 1 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

variable        tdiff equal c_Thot-c_Tcold
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo_modify   colname c_Thot Temp_hot colname c_Tcold Temp_cold                 colname f_hot E_hot colname f_cold E_cold                 colname v_tdiff dTemp_step
thermo          1000
run             10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.906 | 3.906 | 3.906 Mbytes
   Step          Temp         Temp_hot      Temp_cold        E_hot          E_cold       dTemp_step  
      1000   1.35           1.431295       1.2955644     -0             -0              0.13573065   
      2000   1.3593243      1.6602094      1.0898701     -0.13903162     0.14234352     0.57033928   
      3000   1.3412163      1.6308839      1.0677742     -0.2214765      0.25871329     0.56310968   
      4000   1.3275359      1.5248034      1.0792345     -0.26908328     0.34211202     0.44556887   
      5000   1.3230922      1.6266046      1.0523802     -0.33175886     0.43533756     0.5742244    
      6000   1.3037036      1.6021737      1.0408166     -0.3639815      0.49869333     0.56135712   
      7000   1.2903225      1.5701119      1.0603548     -0.40000421     0.55547714     0.50975712   
      8000   1.3050677      1.6420218      1.0221774     -0.46368839     0.60293974     0.61984444   
      9000   1.2950977      1.7153984      1.0583242     -0.51871512     0.66389344     0.65707419   
     10000   1.3100216      1.6680668      1.0871293     -0.57485359     0.7161839      0.58093752   
     11000   1.297052       1.6486494      1.088903      -0.60276081     0.75900024     0.55974633   
Loop time of 12.8698 on 8 procs for 10000 steps with 8000 atoms

Performance: 335670.145 tau/day, 777.014 timesteps/s
99.0% CPU use with 8 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.6624     | 5.5614     | 6.4055     |  30.4 | 43.21
Neigh   | 2.3761     | 2.7104     | 3.0796     |  19.6 | 21.06
Comm    | 0.8473     | 1.9587     | 3.0217     |  68.6 | 15.22
Output  | 0.00068778 | 0.00099949 | 0.0025433  |   0.0 |  0.01
Modify  | 2.2811     | 2.3753     | 2.4584     |   3.8 | 18.46
Other   |            | 0.2629     |            |       |  2.04

Nlocal:           1000 ave        1112 max         841 min
Histogram: 1 1 0 2 0 0 0 0 1 3
Nghost:        2294.38 ave        2506 max        2077 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Neighs:        27441.9 ave       32651 max       19438 min
Histogram: 1 1 0 2 0 0 0 0 0 4

Total # of neighbors = 219535
Ave neighs/atom = 27.441875
Neighbor list builds = 1674
Dangerous builds = 0

# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation

compute         ke all ke/atom
variable        temp atom c_ke/1.5

fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 1 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

fix             ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
thermo_modify   colname c_Thot Temp_hot colname c_Tcold Temp_cold                 colname f_hot E_hot colname f_cold E_cold                 colname v_tdiff dTemp_step colname f_ave dTemp

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix             2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin

variable start_time equal time
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-55)/(lx*ly)/2.0)*(lz/2.0)/f_ave

run             20000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.156 | 4.157 | 4.159 Mbytes
   Step          Temp         Temp_hot      Temp_cold        E_hot          E_cold       dTemp_step       dTemp     
     11000   1.297052       1.6473904      1.088903      -0             -0              0.55848738     0            
     12000   1.2792808      1.6043738      1.0658375     -0.012256975    0.04611547     0.53853632     0.54492428   
     13000   1.2787101      1.7035572      1.1159037     -0.073806664    0.099529002    0.58765348     0.5581748    
     14000   1.289918       1.4642237      1.1073937     -0.11428779     0.13931657     0.35683005     0.56816328   
     15000   1.2932964      1.5032665      1.0523148     -0.17247717     0.19001309     0.45095174     0.57436291   
     16000   1.3025037      1.5424316      1.1185175     -0.22598282     0.22640921     0.42391405     0.56973168   
     17000   1.3009667      1.5582105      1.0745661     -0.27544101     0.26143452     0.48364439     0.5700118    
     18000   1.2970255      1.5019842      1.0228322     -0.31195285     0.31203237     0.479152       0.56544644   
     19000   1.2880631      1.5290587      1.0976483     -0.34645573     0.34243366     0.43141047     0.56338309   
     20000   1.3119675      1.6284144      1.1102294     -0.40922326     0.39217092     0.51818503     0.56614474   
     21000   1.2838063      1.6670934      0.97721382    -0.43809329     0.46021572     0.68987962     0.5686161    
     22000   1.2925041      1.7050682      1.0984963     -0.4871305      0.50520177     0.6065719      0.57226368   
     23000   1.2746463      1.6388503      1.0286701     -0.51212873     0.56478515     0.6101802      0.57290996   
     24000   1.2745381      1.7085713      1.1362975     -0.54529463     0.58540408     0.57227375     0.57296767   
     25000   1.2776401      1.5259253      1.0415158     -0.58389862     0.62623289     0.48440948     0.57386374   
     26000   1.2661888      1.4760829      0.99145001    -0.62638032     0.68155754     0.48463289     0.57021631   
     27000   1.2923677      1.6070495      1.0300276     -0.70014343     0.70236265     0.5770219      0.57001637   
     28000   1.2961449      1.7052335      1.0805793     -0.74856241     0.75775659     0.62465427     0.56927907   
     29000   1.2969474      1.5520176      1.1249649     -0.78900962     0.79539202     0.42705264     0.56986986   
     30000   1.2900596      1.6556864      1.0302676     -0.84180996     0.87187683     0.6254189      0.57245841   
     31000   1.2923209      1.6752068      1.0156911     -0.89036148     0.88285227     0.65951571     0.57358134   
Loop time of 26.7885 on 8 procs for 20000 steps with 8000 atoms

Performance: 322526.365 tau/day, 746.589 timesteps/s
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 8.7499     | 11.122     | 13.336     |  57.7 | 41.52
Neigh   | 4.4966     | 5.3849     | 6.2482     |  33.9 | 20.10
Comm    | 1.6944     | 4.5797     | 7.4844     | 118.6 | 17.10
Output  | 0.0026407  | 0.0029145  | 0.0048103  |   1.3 |  0.01
Modify  | 4.9295     | 5.0982     | 5.1704     |   3.6 | 19.03
Other   |            | 0.6013     |            |       |  2.24

Nlocal:           1000 ave        1118 max         875 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost:        2298.62 ave        2535 max        2063 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs:        27462.4 ave       32904 max       21333 min
Histogram: 2 2 0 0 0 0 0 0 0 4

Total # of neighbors = 219699
Ave neighs/atom = 27.462375
Neighbor list builds = 3340
Dangerous builds = 0
print           "Running average thermal conductivity: $(v_kappa:%.2f)"
Running average thermal conductivity: 3.29
Total wall time: 0:00:40
